Facioscapulohumeral muscular dystrophy (FSHD) is a progressive neuromuscular disorder caused by contractions of repetitive elements within the macrosatellite D4Z4 on chromosome 4q35. There is currently no effective treatment available for FSHD and clinical trials with novel therapeutics have been discouraged by the lack of a recognized mouse model. Clinical trials have also been discouraged by the fact that FSHD is a highly variable and slowly progressing disease whereas the efficacy of therapeutic interventions is ideally established over short periods of time. Therefore, molecular biomarkers of FSHD that could be used to assay responsiveness to therapy would greatly facilitate FSHD therapeutic development and clinical research. High-density oligonucleotide arrays reliably quantify the expression levels of thousands of genes simultaneously and enable identification of such biomarkers.